Alignment-independent sequence analysis based on interval distribution: Application to subtyping and classification of viral sequences

Abstract

Viral sequence classification has widespread applications in structural and functional categorization, clinical and epidemiological studies. Most approaches of subtyping and classification depends on an initial alignment step to asses similarity score followed by distance-based phylogenetic or statistical algorithms. We observe that interval distributions of nucleotide(s) over the sequence possess the potential for sequence comparison and devise an algorithm that determines the similarity/dissimilarity score among pairs of sequences. Classification of HIV virus subtyping by the method obtains exact tally with its biological taxonomy.